GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Williamsia sterculiae CPCC 203464

Align The glucose uptake porter, GluP (characterized)
to candidate WP_083709761.1 BW971_RS11095 sugar porter family MFS transporter

Query= TCDB::Q0SE66
         (483 letters)



>NCBI__GCF_900156495.1:WP_083709761.1
          Length = 504

 Score =  458 bits (1178), Expect = e-133
 Identities = 236/454 (51%), Positives = 317/454 (69%), Gaps = 7/454 (1%)

Query: 26  IAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSALLGFAIASALLGAAAGAMLAGRIAD 85
           + V AA+GG LFG+DS+V+NGAV +I+G F +   + GFA+A ALLG A GA  AGR+AD
Sbjct: 44  VTVAAAVGGFLFGFDSSVVNGAVDSIKGHFALSEFVTGFAVAIALLGCAVGAWFAGRLAD 103

Query: 86  RYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIAEISPAR 145
            +GR   M   +++F+ S+IGT F  ++  L+ +R++GG+G+G+ASVIAPAYIAEI+PAR
Sbjct: 104 VWGRKRVMLLGSLLFVASSIGTAFCFSLGDLLFWRVLGGLGIGIASVIAPAYIAEIAPAR 163

Query: 146 VRGRLGSLQQLAIVTGIFVSLLVDYALAAIAGGSQEELWFGLEAWRWMFLAMCVPALAYG 205
            RG LGSLQQLAI  GIF++LL D  L   AG +   LW G+EAWRWMFL   +PA+ YG
Sbjct: 164 FRGALGSLQQLAITIGIFIALLSDSLLQDSAGAAANTLWLGVEAWRWMFLVGVIPAVIYG 223

Query: 206 LLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRSTLARETQPSIRDLKGS 265
           +L+L IPESPRYL+      EA  IL  + GE+    +++ IR TL RE++ SIRD++G 
Sbjct: 224 VLALLIPESPRYLVGNHLDEEAARILTEVTGEQNPLERVKEIRLTLVRESKASIRDIRGP 283

Query: 266 AFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVITSVVNIATTL 325
           +FGL P VW+GI L+VFQQFVGIN IFYYS+ LW +VGF E  S + +VIT+V+N+  T 
Sbjct: 284 SFGLHPFVWVGIWLAVFQQFVGINAIFYYSTTLWSSVGFSESDSFKTSVITAVINVVMTF 343

Query: 326 IAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTGLQGPIALVA 385
            +I ++DR GRR +L+IGS GM V L  +A +  T      D +T P   G+   IAL+ 
Sbjct: 344 GSILFVDRFGRRRMLLIGSVGMFVGL-LLACVAFTQQIGSGDKITLPDPWGV---IALIG 399

Query: 386 ANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTFPSMKDFSLG 445
           ANLFV+AF  +WGP++WV+LGE FPNR+R  AL +   A W AN+ IT+ FP +   S+G
Sbjct: 400 ANLFVIAFAATWGPILWVMLGEMFPNRLRGVALGVCTAANWVANFAITLLFPELNS-SIG 458

Query: 446 IS--YGFYAVCAVLSLVFVLRWVKETKGVELEAM 477
           ++  YGF+A CA  S +FV   V ETKG+ELEAM
Sbjct: 459 LAWIYGFFAFCAAASFLFVQFKVPETKGMELEAM 492


Lambda     K      H
   0.324    0.138    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 731
Number of extensions: 37
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 483
Length of database: 504
Length adjustment: 34
Effective length of query: 449
Effective length of database: 470
Effective search space:   211030
Effective search space used:   211030
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory